Ph.D. (Physics) Korea Advanced Institute of Science and Techonology, Korea
2000
M.S. (Physics) Korea Advanced Institute of Science and Techonology, Korea
1998
B.S. (Physics) Korea Advanced Institute of Science and Techonology, Korea
RESEARCH AND TEACHING EXPERIENCES
2015-present
Technical Scientist, RIKEN Theoretical Molecular Science Laboratory, Japan
2010-present
Research Scientist, RIKEN Advanced Institute for Computational Science, Japan
2010
Assistant Professor Extraordinary, Graduate School of System Informatics, Kobe University, Japan
2009
Assistant Professor Extraordinary, Graduate School of Engineering, Kobe University, Japan
2006
Post Doctor, Graduate School of Information Science, Nagoya University, Japan
2005
Post Doctor, Department of Chemistry, Korea Institute of Science and Technology, Korea
PROFESSIONAL AFFILIATIONS
The Biophysical Society of Japan, Japan Society for Molecular Science
RESEARCH PROJECTS
Development of parallel Molecular Dynamics program
Development of QM/MM program and simulations of the enzyme reactions
PUBLICATIONS
J. Jung, C. Kobayashi, Y. Sugita., "Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation" J. Chem. Phys., 148, 164109 (2018)
C. Kobayashi*, J. Jung*, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, M. Kamiya, Y. Sugita., "GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms" J. Comput. Chem. (2017) 38, 2193-2206 (*equally contributed)
J. Jung, Y. Sugita, "Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems", J. Comput. Chem. (2017) 38, 1410-1418.
J. Jung, A. Naruse, C. Kobayashi, Y. Sugita, "Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations", J. Chem. Theory Comput. (2016) 12, 4947-4958
Matsunaga, Y., Komuro, Y., Kobayashi, C., Jung, J., Mori, T., Sugita, Y. Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein. (2016) J. Phys. Chem. Lett. 7: 1446–1451.
Jung, J., Kobayashi, C., Imamura, T., Sugita, Y. Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations. (2016) Comput. Phys. Comm. 200:57-65.
Jung, J.*, Mori, T.*, Kobayashi, C., Matsunaga, Y., Yoda, T., Feig, M., Sugita, Y. GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations. (2015) WIREs Comput. Mol. Sci. 5: 310-323. (* equally contributed)
Jung, J., Mori, T., Sugita, Y. Midpoint Cell Method for Hybrid (MPI+OpenMP) Parallelization of Molecular Dynamics Simulations. (2014) J. Comp. Chem.35: 1064-1072.
Mori, T., Jung, J., Sugita, Y. Surface-tension replica-exchange molecular dynamics method for enhanced sampling of biological membrane systems. (2013) J. Chem. Theory Comput. 9: 5629-5640.
Jung, J., Mori, T., Sugita, Y. Efficient lookup table using a linear function of inverse distance squared. (2013) J. Comput. Chem. 34: 2412-2420.
Jung, J., Re, S., Sugita, Y., Ten-no, S. Improved constrained optimization method for reaction-path determination in quantum mechanical/molecular mechanical calculations. (2013) J. Chem. Phys. 138: 044106 (10 pages).
Kitagawa, Y., Akinaga, Y., Kawashima, Y., Jung, J., Ten-no, S. A QM/MM-MD study on protein electronic properties: Circular dichroism spectra of oxytocin and insulin. (2012) Chem. Phys. 401: 95-102.
Akinaga, Y., Jung, J., Ten-no, S. QM/MM calculation of protein magnetic shielding tensors with generalized hybrid-orbital method: A GIAO approach. (2011) Phys. Chem. Chem. Phys. 13:14490-14499.
Kawashima, Y., Nakano, H., Jung, J., Ten-no, S. A combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals : Implementation for electronic excited states. (2011) Phys. Chem. Chem. Phys. 13:11731-11738.
Re, S., Imai, T., Jung, J., Ten-no, S., Sugita, Y. Geometrically Associative Yet Electronically Dissociative Character in the Transition State of Enzymatic Reversible Phosphorylation. (2011) J. Comput. Chem. 32:260–270.
Jung, J., Sugita, Y., Ten-no, S. Møller-Plesset gradient implementation in the generalized hybrid orbital (GHO) method. (2010) J. Chem. Phys. 132: 084106 (6 pages).
Jung, J., Bugals, A.J., Lee, E. Topological quantities determining the folding/unfolding rate of two-state folding proteins. (2010) J. Sol. Chem. 39:943-958.
Jung, J., Ten-no, S. Simple avoidance of Pauli repulsion errors in the generalized hybrid orbital (GHO) method. (2010) Chem. Phys. Lett. 484:344-348.
Ten-no, S., Jung, J., Chuman, H., Kawashima, Y. Assessment of free energy expressions in RISM integral equation theory: Theoretical prediction of partition coefficients revisited. (2010) Mol. Phys. 108:327-332.
Re, S., Jung, J., Ten-no, S., Sugita, Y. A two-dimensional energy surface of the phosphoryl transfer reaction catalyzed by phosphoserine phosphatase. (2009) Chem. Phys. Lett. 480:284-288.
Jung, J., Choi, C.H., Sugita, Y., Ten-no, S. New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals. (2007) J. Chem. Phys. 127:204102 (12 pages).
Jung, J., Lee, J., Moon, H. Topological Determinants of protein unfolding rates. (2005) Proteins:Structure, Function, and Bioinformatics 58:389-395.
Jung, J., Lee, J., Moon, H. Identification of the Protein Native Structure by Using a Sequence-Dependent Feature in Contact Maps. (2005) J. Korean Phys. Soc. 46:625-630.
